Contrasted host specificity of gut and endosymbiont bacterial communities in alpine grasshoppers and crickets.

Bacteria colonize the body of macroorganisms to form associations ranging from parasitic to mutualistic. Endosymbiont and gut symbiont communities are distinct microbiomes whose compositions are influenced by host ecology and evolution. Although the composition of horizontally acquired symbiont communities can correlate to host species identity (i.e. harbor host specificity) and host phylogeny (i.e. harbor phylosymbiosis), we hypothesize that the microbiota structure of vertically inherited symbionts (e.g. endosymbionts like Wolbachia) is more strongly associated with the host species identity and phylogeny than horizontally acquired symbionts (e.g. most gut symbionts). Here, using 16S metabarcoding on 336 guts from 24 orthopteran species (grasshoppers and crickets) in the Alps, we observed that microbiota correlated to host species identity, i.e. hosts from the same species had more similar microbiota than hosts from different species. This effect was ~5 times stronger for endosymbionts than for putative gut symbionts. Although elevation correlated with microbiome composition, we did not detect phylosymbiosis for endosymbionts and putative gut symbionts: closely related host species did not harbor more similar microbiota than distantly related species. Our findings indicate that gut microbiota of studied orthopteran species is more correlated to host identity and habitat than to the host phylogeny. The higher host specificity in endosymbionts corroborates the idea that-everything else being equal-vertically transmitted microbes harbor stronger host specificity signal, but the absence of phylosymbiosis suggests that host specificity changes quickly on evolutionary time scales

Long-term quality of life after en-bloc vertebrectomy: 25 patients followed up for 9 years

AbstractObjectiveAssess quality-of-life results in patients who have undergone extensive curative surgery for spinal tumor and compare them to the general population in France.IntroductionLife expectancy is not the only criterion to assess the outcomes after massive tumor resections. Residual quality of life is also crucial. An indication for major surgery for spinal tumor should take the patient's long-term functional status into account, but the literature is limited on this question.Materials and methodsTwenty-five living patients from a group of 120 operated were assessed, all of whom were operated on by the same surgeon between 1984 and 2007. The mean follow-up was 9 years (range, 3–25 years). The mean age at surgery was 49 years. The patients completed different functional and quality-of-life questionnaires: the Oswestry Disability Index version 2 (ODI), the PROLO, the Karnofsky Index of performance status (KI), the Eastern Cooperative Oncology Group performance status (ECOG), the Short Form-36 Health Survey (SF-36), and the EuroQol-5 Dimensions (EQ5D). In addition, each patient was clinically and radiographically evaluated. Subgroups were identified considering the number of levels resected and histology. Their results on the SF-36 were compared with the results from the general population in France.ResultsThe mean PCS (physical component summary of the SF-36) was 52.4, the MCS (mental component summary, the psychological component of the SF-36) was 47.7, the ODI was 18.2, the PROLO was 7, the ECOG was 1, and the KI was 80%. The resections at three levels were associated with worse results in terms of quality of life, but overall, the results were similar to the French general population data for all categories of the SF-36.ConclusionAppropriate indications for massive spinal resection give good oncological and functional results. Although the expected life expectancy justifies this aggressive surgery, postoperative quality of life shows that it can also be successful on a functional level.Level of evidenceLevel IV; retrospective clinical study

Breaking the silence of the 500-year-old smiling garden of everlasting flowers: The En Tibi book herbarium

We reveal the enigmatic origin of one of the earliest surviving botanical collections. The 16th-century Italian En Tibi herbarium is a large, luxurious book with c. 500 dried plants, made in the Renaissance scholarly circles that developed botany as a distinct discipline. Its Latin inscription, translated as “Here for you a smiling garden of everlasting flowers”, suggests that this herbarium was a gift for a patron of the emerging botanical science. We follow an integrative approach that includes a botanical similarity estimation of the En Tibi with contemporary herbaria (Aldrovandi, Cesalpino, “Cibo”, Merini, Estense) and analysis of the book’s watermark, paper, binding, handwriting, Latin inscription and the morphology and DNA of hairs mounted under specimens. Rejecting the previous origin hypothesis (Ferrara, 1542–1544), we show that the En Tibi was made in Bologna around 1558. We attribute the En Tibi herbarium to Francesco Petrollini, a neglected 16th-century botanist, to whom also belongs, as clarified herein, the controversial “Erbario Cibo” kept in Rome. The En Tibi was probably a work on commission for Petrollini, who provided the plant material for the book. Other people were apparently involved in the compilation and offering of this precious gift to a yet unknown person, possibly the Habsburg Emperor Ferdinand I. The En Tibi herbarium is a Renaissance masterpiece of art and science, representing the quest for truth in herbal medicine and botany. Our multidisciplinary approach can serve as a guideline for deciphering other anonymous herbaria, kept safely “hidden” in treasure rooms of universities, libraries and museums

Structural Features of Single-Stranded Integron Cassette attC Sites and Their Role in Strand Selection

We recently showed that cassette integration and deletion in integron platforms were occurring through unconventional site-specific recombination reactions involving only the bottom strand of attC sites. The lack of sequence conservation among attC sites led us to hypothesize that sequence-independent structural recognition determinants must exist within attC sites. The structural data obtained from a synaptic complex of the Vibrio cholerae integrase with the bottom strand of an attC site has shown the importance of extra helical bases (EHB) inside the stem-loop structure formed from the bottom strand. Here, we systematically determined the contribution of three structural elements common to all known single-stranded attC site recombination substrates (the EHBs, the unpaired central spacer (UCS), and the variable terminal structure (VTS)) to strand choice and recombination. Their roles have been evaluated in vivo in the attl x attC reaction context using the suicide conjugation assay we previously developed, but also in an attC x attC reaction using a deletion assay. Conjugation was used to deliver the attC sites in single-stranded form. Our results show that strand choice is primarily directed by the first EHB, but the presence of the two other EHBs also serves to increase this strand selection. We found that the structure of the central spacer is essential to achieve high level recombination of the bottom strand, suggesting a dual role for this structure in active site exclusion and for hindering the reverse reaction after the first strand exchange. Moreover, we have shown that the VTS has apparently no role in strand selectivity

Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field

Protists are abundant, diverse and perform essential functions in soils. Protistan community structure and its change across time or space are traditionally studied at the species level but the relative importance of the processes shaping these patterns depends on the taxon phylogenetic resolution. Using 18S rDNA amplicon data of the Cercozoa, a group of dominant soil protists, from an agricultural field in western Germany, we observed a turnover of relatively closely related taxa (from sequence variants to genus‐level clades) across soil depth; while across soil habitats (rhizosphere, bulk soil, drilosphere), we observed turnover of relatively distantly related taxa, confirming Paracercomonadidae as a rhizosphere‐associated clade. We extended our approach to show that closely related Cercozoa encounter divergent arbuscular mycorrhizal (AM) fungi across soil depth and that distantly related Cercozoa encounter closely related AM fungi across soil compartments. This study suggests that soil Cercozoa community assembly at the field scale is driven by niche‐based processes shaped by evolutionary legacy of adaptation to conditions primarily related to the soil compartment, followed by the soil layer, giving a deeper understanding on the selection pressures that shaped their evolution

The relative importance of ecological drivers of arbuscularmycorrhizal fungal distribution varies with taxon phylogeneticresolution

The phylogenetic depth at which arbuscular mycorrhizal (AM) fungi harbor a coherent eco-logical niche is unknown, which has consequences for operational taxonomic unit (OTU)delineation from sequence data and the study of their biogeography. We tested how changes in AM fungi community composition across habitats (beta diver-sity) vary with OTU phylogenetic resolution. We inferred exact sequence variants (ESVs) toresolve phylotypes at resolutions finer than provided by traditional sequence clustering andanalyzed beta diversity profiles up to order-level sequence clusters. At the ESV level, we detected the environmental predictors revealed with traditional OTUsor at higher genetic distances. However, the correlation between environmental predictorsand community turnover steeply increased at a genetic distance ofc. 0.03 substitutions persite. Furthermore, we observed a turnover of either closely or distantly related taxa (respec-tively at or above 0.03 substitutions per site) along different environmental gradients. This study suggests that different axes of AM fungal ecological niche are conserved at dif-ferent phylogenetic depths. Delineating AM fungal phylotypes using DNA sequences shouldscreen different phylogenetic resolutions to better elucidate the factors that shape communi-ties and predict the fate of AM symbioses in a changing environment

Pseudo-Random Streams for Distributed and Parallel Stochastic Simulations on GP-GPU

International audienceRandom number generation is a key element of stochastic simulations. It has been widely studied for sequential applications purposes, enabling us to reliably use pseudo-random numbers in this case. Unfortunately, we cannot be so enthusiastic when dealing with parallel stochastic simulations. Many applications still neglect random stream parallelization, leading to potentially biased results. In particular parallel execution platforms, such as Graphics Processing Units (GPUs), add their constraints to those of Pseudo-Random Number Generators (PRNGs) used in parallel. This results in a situation where potential biases can be combined with performance drops when parallelization of random streams has not been carried out rigorously. Here, we propose criteria guiding the design of good GPU-enabled PRNGs. We enhance our comments with a study of the techniques aiming to parallelize random streams correctly, in the context of GPU-enabled stochastic simulations

Comparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains

Strains of the freshwater cyanobacterium Synechococcus elongatus were first isolated approximately 60 years ago, and PCC 7942 is well established as a model for photosynthesis, circadian biology, and biotechnology research. The recent isolation of UTEX 3055 and subsequent discoveries in biofilm and phototaxis phenotypes suggest that lab strains of S. elongatus are highly domesticated. We performed a comprehensive genome comparison among the available genomes of S. elongatus and sequenced two additional laboratory strains to trace the loss of native phenotypes from the standard lab strains and determine the genetic basis of useful phenotypes. The genome comparison analysis provides a pangenome description of S. elongatus, as well as correction of extensive errors in the published sequence for the type strain PCC 6301. The comparison of gene sets and single nucleotide polymorphisms (SNPs) among strains clarifies strain isolation histories and, together with large-scale genome differences, supports a hypothesis of laboratory domestication. Prophage genes in laboratory strains, but not UTEX 3055, affect pigmentation, while unique genes in UTEX 3055 are necessary for phototaxis. The genomic differences identified in this study include previously reported SNPs that are, in reality, sequencing errors, as well as SNPs and genome differences that have phenotypic consequences. One SNP in the circadian response regulator rpaA that has caused confusion is clarified here as belonging to an aberrant clone of PCC 7942, used for the published genome sequence, that has confounded the interpretation of circadian fitness research

PP/PP-HI/silica nanocomposites for HVDC cable insulation: Are silica clusters beneficial for space charge accumulation?

New potential High Voltage Direct Current (HVDC) cable insulation materials based on nanocomposites are developed in this study. The nanocomposites are produced by blending of polypropylene (PP), propylene-ethylene copolymer (PP–HI) and a modified fumed silica (A-silica) in a concentration of 1 and 2 wt %. The A-silica is successfully modified with (3-aminopropyl)triethoxysilane (APTES) via a solvent-free method, as proven by infrared spectroscopy, thermogravimetry and transmission electron microscope mapping. A-silica in the polymer matrix acts as a nucleating agent resulting in an increase of the crystallization temperature of the polymers and a smaller crystal size. Moreover, the silica addition modified the crystals morphology of the unfilled PP/PP-HI blend. The composite containing A-silica with 2 wt% contains bigger-size silica clusters than the composite filled with 1 wt%. The composite with the higher A-silica concentration shows lower space charge accumulation and a lower charge current value. Besides, much deeper traps and lower trap density are observed in the composite with 2 wt% A-silica addition compared to the one with a lower concentration. Surprisingly, the presence of silica clusters with dimensions of more than 200 nm exhibit a positive effect on reducing the space charge accumulation. However, the real cause of this improvement might be due to change of the electron distribution stemming from the amine-amine hydrogen bond formation, or the change of the chain mobility due to the presence of occluded polymer macromolecules constrained inside the high structure silica clusters. Both phenomena may lead to a higher energetic barrier of charge de-trapping, thus increasing the depth of the charge traps

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

In fast-growing bacteria, the genomic location of ribosomal protein (RP) genes is biased towards the replication origin (oriC). This trait allows optimizing their expression during exponential phase since oriC neighboring regions are in higher dose due to multifork replication. Relocation of s10-spc-α locus (S10), which codes for most of the RP, to ectopic genomic positions shows that its relative distance to the oriC correlates to a reduction on its dosage, its expression, and bacterial growth rate. However, a mechanism linking S10 dosage to cell physiology has still not been determined.We hypothesized that S10 dosage perturbations impact protein synthesis capacity. Strikingly, we observed that in Vibrio cholerae, protein production capacity was independent of S10 position. Deep sequencing revealed that S10 relocation altered chromosomal replication dynamics and genome-wide transcription. Such changes increased as a function of oriC-S10 distance. Since RP constitutes a large proportion of cell mass, lower S10 dosage could lead to changes in macromolecular crowding, impacting cell physiology. Accordingly, cytoplasm fluidity was higher in mutants where S10 is most distant from oriC. In hyperosmotic conditions, when crowding differences are minimized, the growth rate and replication dynamics were highly alleviated in these strains.The genomic location of RP genes ensures its optimal dosage. However, besides of its essential function in translation, their genomic position sustains an optimal macromolecular crowding essential for maximizing growth. Hence, this could be another mechanism coordinating DNA replication to bacterial growth.Fil: Soler Bistue, Alfonso J. C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Aguilar Pierlé, Sebastián. Institut Pasteur; FranciaFil: Garcia Garcerá, Marc. Institut Pasteur; FranciaFil: Val, Marie Eve. Institut Pasteur; FranciaFil: Sismeiro, Odile. Institut Pasteur; FranciaFil: Varet, Hugo. Institut Pasteur; FranciaFil: Sieira, Rodrigo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; ArgentinaFil: Krin, Evelyne. Institut Pasteur; FranciaFil: Skovgaard, Ole. Roskilde Universitet; DinamarcaFil: Comerci, Diego José. Universidad Nacional de San Martin. Instituto de Investigaciones Biotecnologicas. - Consejo Nacional de Investigaciones Cientificas y Tecnicas. Oficina de Coordinacion Administrativa Pque. Centenario. Instituto de Investigaciones Biotecnologicas.; ArgentinaFil: Rocha, Eduardo P. C.. Institut Pasteur; FranciaFil: Mazel, Didier. Institut Pasteur; Franci